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protein metals Protein-protein interface(s) links
Hydrolase PDB id
2ki7
Jmol
Contents
Protein chains
111 a.a. *
97 a.a. *
Metals
_ZN
* Residue conservation analysis
PDB id:
2ki7
Name: Hydrolase
Title: The solution structure of rpp29-rpp21 complex from pyrococcus furiosus
Structure: Ribonuclease p protein component 1. Chain: a. Synonym: rnase p component 1. Engineered: yes. Ribonuclease p protein component 4. Chain: b. Synonym: rnase p component 4. Engineered: yes
Source: Pyrococcus furiosus dsm 3638. Organism_taxid: 186497. Strain: dsm3638 / jcm 8422 / vc1. Atcc: 43587. Gene: rnp1, pf1816. Expressed in: escherichia coli. Expression_system_taxid: 562. Gene: rnp4, pf1613.
NMR struc: 10 models
Authors: Y.Xu,M.P.Foster
Key ref: Y.Xu et al. (2009). Solution structure of an archaeal RNase P binary protein complex: formation of the 30-kDa complex between Pyrococcus furiosus RPP21 and RPP29 is accompanied by coupled protein folding and highlights critical features for protein-protein and protein-RNA interactions. J Mol Biol, 393, 1043-1055. PubMed id: 19733182 DOI: 10.1016/j.jmb.2009.08.068
Date:
28-Apr-09     Release date:   15-Sep-09    
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q8U007  (RNP1_PYRFU) -  Ribonuclease P protein component 1
Seq:
Struc: 		127 a.a.
111 a.a.
Protein chain
Pfam   ArchSchema ?
Q8U0H6  (RNP4_PYRFU) -  Ribonuclease P protein component 4
Seq:
Struc: 		117 a.a.
97 a.a.
Key:    PfamA domain  Secondary structure

 Enzyme reactions 
   Enzyme class: Chains A, B: E.C.3.1.26.5  - Ribonuclease P.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Endonucleolytic cleavage of RNA, removing 5'-extra-nucleotide from tRNA precursor.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     ribonuclease P complex   2 terms 
  Biological process     rRNA processing   4 terms 
  Biochemical function     hydrolase activity     4 terms  

 

 
DOI no: 10.1016/j.jmb.2009.08.068 J Mol Biol 393:1043-1055 (2009)
PubMed id: 19733182  
 
 
Solution structure of an archaeal RNase P binary protein complex: formation of the 30-kDa complex between Pyrococcus furiosus RPP21 and RPP29 is accompanied by coupled protein folding and highlights critical features for protein-protein and protein-RNA interactions.
Y.Xu, C.D.Amero, D.K.Pulukkunat, V.Gopalan, M.P.Foster.
 
  ABSTRACT  
 
Ribonuclease P (RNase P) is a ribonucleoprotein (RNP) enzyme that catalyzes the Mg(2+)-dependent 5' maturation of precursor tRNAs. In all domains of life, it is a ribozyme: the RNase P RNA (RPR) component has been demonstrated to be responsible for catalysis. However, the number of RNase P protein subunits (RPPs) varies from 1 in bacteria to 9 or 10 in eukarya. The archaeal RPR is associated with at least 4 RPPs, which function in pairs (RPP21-RPP29 and RPP30-POP5). We used solution NMR spectroscopy to determine the three-dimensional structure of the protein-protein complex comprising Pyrococcus furiosus RPP21 and RPP29. We found that the protein-protein interaction is characterized by coupled folding of secondary structural elements that participate in interface formation. In addition to detailing the intermolecular contacts that stabilize this 30-kDa binary complex, the structure identifies surfaces rich in conserved basic residues likely vital for recognition of the RPR and/or precursor tRNA. Furthermore, enzymatic footprinting experiments allowed us to localize the RPP21-RPP29 complex to the specificity domain of the RPR. These findings provide valuable new insights into mechanisms of RNP assembly and serve as important steps towards a three-dimensional model of this ancient RNP enzyme.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20935047 S.Sinapah, S.Wu, Y.Chen, B.M.Pettersson, V.Gopalan, and L.A.Kirsebom (2011).
Cleavage of model substrates by archaeal RNase P: role of protein cofactors in cleavage-site selection.
  Nucleic Acids Res, 39, 1105-1116.  
20334683 F.J.Sun, and G.Caetano-Anollés (2010).
The ancient history of the structure of ribonuclease P and the early origins of Archaea.
  BMC Bioinformatics, 11, 153.  
20215441 K.L.Hands-Taylor, L.Martino, R.Tata, J.J.Babon, T.T.Bui, A.F.Drake, R.L.Beavil, G.J.Pruijn, P.R.Brown, and M.R.Conte (2010).
Heterodimerization of the human RNase P/MRP subunits Rpp20 and Rpp25 is a prerequisite for interaction with the P3 arm of RNase MRP RNA.
  Nucleic Acids Res, 38, 4052-4066.  
19931535 L.B.Lai, A.Vioque, L.A.Kirsebom, and V.Gopalan (2010).
Unexpected diversity of RNase P, an ancient tRNA processing enzyme: challenges and prospects.
  FEBS Lett, 584, 287-296.  
21135215 L.B.Lai, P.P.Chan, A.E.Cozen, D.L.Bernick, J.W.Brown, V.Gopalan, and T.M.Lowe (2010).
Discovery of a minimal form of RNase P in Pyrobaculum.
  Proc Natl Acad Sci U S A, 107, 22493-22498.  
20716516 N.Jarrous, and V.Gopalan (2010).
Archaeal/eukaryal RNase P: subunits, functions and RNA diversification.
  Nucleic Acids Res, 38, 7885-7894.  
20627997 O.Esakova, and A.S.Krasilnikov (2010).
Of proteins and RNA: the RNase P/MRP family.
  RNA, 16, 1725-1747.  
20139629 T.Honda, T.Hara, J.Nan, X.Zhang, and M.Kimura (2010).
Archaeal homologs of human RNase P protein pairs Pop5 with Rpp30 and Rpp21 with Rpp29 work on distinct functional domains of the RNA subunit.
  Biosci Biotechnol Biochem, 74, 266-273.  
20705647 W.Y.Chen, D.K.Pulukkunat, I.M.Cho, H.Y.Tsai, and V.Gopalan (2010).
Dissecting functional cooperation among protein subunits in archaeal RNase P, a catalytic ribonucleoprotein complex.
  Nucleic Acids Res, 38, 8316-8327.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time.